Repositories list

• PTMVision

  Public
  Web application for the interactive visualization of post-translational modifications of proteins from open search software.

  web-applicationproteomicsvisual-analytics+ 1post-translational-modification

  HTML

  •

  GNU General Public License v3.0

  •0•4•0•0•Updated Jul 30, 2025Jul 30, 2025

• Evidente2.0

  Public
  Go

  •1•1•27•1•Updated Jul 25, 2025Jul 25, 2025

• Nextstrain-TrepoGen

  Public
  Nextstrain TrepoGen is a reproducible Nextstrain workflow for tracking bacterial diversity at both genome- and gene-level.

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jul 21, 2025Jul 21, 2025

• tsne

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jul 15, 2025Jul 15, 2025

• VIPurPCA

  Public
  Jupyter Notebook

  •

  MIT License

  •0•1•1•0•Updated Jul 4, 2025Jul 4, 2025

• phage_host_dual_transcriptomics

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Jul 4, 2025Jul 4, 2025

• MUSIAL

  Public
  Summarize SNV and indel information on single gene or genome level together with other relevant statistics based on .vcf files.

  genomicssequence-alignmentvariant-annotation+ 2variant-analysissequence-generation

  Java

  •

  GNU General Public License v3.0

  •1•5•1•0•Updated Jul 3, 2025Jul 3, 2025

• TSSpredator-Web

  Public
  TSSpredator-Web allows a web-based TSS predicition for prokaryotic data.

  JavaScript

  •

  GNU General Public License v3.0

  •0•1•0•1•Updated Jul 2, 2025Jul 2, 2025

• MUSIAL-WEB

  Public archive
  ⚠️ This repository is deprecated and was archived, please see: https://github.com/Integrative-Transcriptomics/MUSIAL

  JavaScript

  •0•0•0•0•Updated Jun 17, 2025Jun 17, 2025

• tuekitzmed-module

  Public
  JavaScript

  •0•0•0•0•Updated Jun 12, 2025Jun 12, 2025

• phagomics

  Public
  Nextflow

  •0•0•0•0•Updated May 21, 2025May 21, 2025

• preserve-nextflow

  Public
  A repository for the Nextflow Pipeline that optimally predicts the structure of proteins and searches for structural homologs either within a set of references or within the set of provided proteins..

  Nextflow

  •1•1•0•0•Updated May 16, 2025May 16, 2025

• trustpca

  Public
  Python

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Apr 25, 2025Apr 25, 2025

• lipo-search

  Public
  A repository for the Nextflow Pipeline that optimally predicts the structure of Lipoproteins and searches for structural homologs within a set of lipoprotein references.

  MIT License

  •1•0•0•0•Updated Nov 19, 2024Nov 19, 2024

• tss-captur-dsl2-with-RNAseq

  Public
  TSS-characterization pipeline for transcribed but unclassified RNA-transcripts

  HTML

  •

  GNU General Public License v3.0

  •2•0•0•0•Updated Sep 24, 2024Sep 24, 2024

• tss-captur-dsl2

  Public
  TSS-characterization pipeline for transcribed but unclassified RNA-transcripts

  HTML

  •

  GNU General Public License v3.0

  •2•2•0•0•Updated Sep 23, 2024Sep 23, 2024

• manual

  Public
  HTML

  •0•0•0•0•Updated Sep 10, 2024Sep 10, 2024

• tss-prediction-comparison

  Public
  This repository includes the tool for the prediction, comparison and visualization of TSS predicted using RNAseq. The results are then compared to provide an overview and also single-detailed visualizations.

  Jupyter Notebook

  •0•3•14•0•Updated Aug 31, 2024Aug 31, 2024

• GO-Compass

  Public
  Visual Navigation of Multiple Lists of GO terms

  JavaScript

  •0•4•4•18•Updated Apr 3, 2024Apr 3, 2024

• rnaSeq-pipeline-rework

  Public
  Python

  •

  MIT License

  •1•1•0•0•Updated Apr 1, 2024Apr 1, 2024

• ClInt

  Public
  Nextflow

  •0•0•0•0•Updated Feb 16, 2024Feb 16, 2024

• FUNAGE-Pro-processing

  Public
  Python

  •0•0•0•0•Updated Jan 24, 2024Jan 24, 2024

• OmicsTIDE2.0

  Public
  Tool for the analysis of trends in multi-omics data

  JavaScript

  •1•3•2•0•Updated Jan 16, 2024Jan 16, 2024

• DamageProfiler

  Public
  A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage

  ngsdamageadna

  Java

  •

  GNU General Public License v3.0

  •4•18•9•0•Updated Nov 18, 2023Nov 18, 2023

• BLASTphylo

  Public
  JavaScript

  •0•0•0•0•Updated Jun 26, 2023Jun 26, 2023

• phylotree.js

  Public
  Interactive viewer of phylogenetic trees

  JavaScript

  •

  MIT License

  •78•0•0•0•Updated Jun 9, 2023Jun 9, 2023

• tss-captur

  Public
  TSS-characterization pipeline for transcribed but unclassified RNA-transcripts

  Python

  •

  GNU General Public License v3.0

  •2•0•0•0•Updated Apr 5, 2023Apr 5, 2023

• Shiny_DESeq2

  Public
  R

  •0•1•6•0•Updated Apr 3, 2023Apr 3, 2023

• Classico

  Public
  Python

  •0•0•1•0•Updated Mar 31, 2023Mar 31, 2023

• Bio-MedVis-Challenge-IEEE-2022

  Public
  Space to collect prototypes and code for the EpiProteomicsVis challenge @ISMB2022

  JavaScript

  •0•0•1•0•Updated Jan 12, 2023Jan 12, 2023